Genome Analysis of Mycobacterium massiliense Strain M172, Which Contains a Putative Mycobacteriophage

Siew Woh Choo, Aini Mohamed Yusoff, Yan Ling Wong, Wei Yee Wee, Chia Sui Ong, Kee Peng Ng and Yun Fong Ngeow J. Bacteriol. 2012, 194(18):5128. DOI: 10.1128/JB.01096-12. Downloaded from http://jb.asm.org/ on October 1, 2013 by UNIVERSITY OF MALAYA

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GENOME ANNOUNCEMENT

Genome Analysis of Mycobacterium massiliense Strain M172, Which Contains a Putative Mycobacteriophage
Siew Woh Choo,b Aini Mohamed Yusoff,b Yan Ling Wong,a Wei Yee Wee,b Chia Sui Ong,c Kee Peng Ng,a and Yun Fong Ngeowa
Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysiaa; Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysiab; and Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysiac

The genome of Mycobacterium massiliense M172, isolated from a human sputum sample, was sequenced using Illumina GA IIX technology and found to contain 5,204,460 bp, including putative genes for virulence and antibiotic resistance as well as a 92-kb genomic region most likely to correspond to a mycobacteriophage.

ysogeny is found in many mycobacterial species isolated from environmental and clinical sources (6). Of more than 2,400 mycobacteriophages identied so far, only about 360, most of which are from soil samples, have been completely sequenced (Mycobacteriophage Database [http://phagesdb.org]). Mycobacterium massiliense, a subspecies of Mycobacterium abscessus, was rst isolated from the sputum and bronchoalveolar uid of a patient with hemoptoic pneumonia in Marseille, France (1). It is now known to be a frequent cause of bronchopulmonary infections in patients with compromised immunity (4). Strain M172 is a sputum isolate from a Malaysian patient. It was identied as a Mycobacterium massiliense strain by its rpoB and erm41 gene sequences (5, 7), which showed 99.0% and 100% similarity, respectively, to the rpoB and erm41 gene sequences of the reference M. massiliense CIP108297 strain. Raw reads of the M172 genome were generated by using Illumina GA IIx technology, producing 17,156,157 reads. The sequences assembled with Genomics Workbench 5.0 (CLCBio, Aarhus, Denmark) produced 33 contigs, with an N50 contig size of 862,630 bp. The genome size of 5,204,460 bp and GC content of 64% were similar to those of reference M. massiliense strain CIP108297. Annotation results determined with Rapid Annotations using Subsystem Technology (RAST) (3) revealed 5,221 predicted coding sequences, 47 tRNAs, one tRNA pseudogene, and 2 rRNAs. In the coding sequences were 427 genes categorized for amino acids and other derivatives and 339 involved in cofactors, vitamins, prosthetic groups, and pigments. Of 38 genes involved in virulence and defenses, 25 were associated with resistance to antibiotics and toxic compounds. Two genes were associated with dormancy and sporulation, and 58 were linked to phages, prophages, and transposable elements. A large, 92-kb genomic region was observed that did not match with any region in the reference M. abscessus ATCC 19977 genome when sequences were aligned using BLAST program (2). RAST annotations showed the presence of many putative phage-related genes, including genes that code for phage-tail protein, phage endolysin, phage major capsid protein, phage capsid and scaffold, and phage tape measure protein. Both ends of this region were associated with putative open reading frames (ORFs) that code for phage integrase. It is likely that this genomic region belongs to a

bacteriophage that had been inserted into the M172 genome. Work is ongoing to identify the origin of this phage and to examine its effect on the virulence and drug resistance of M172. Nucleotide sequence accession numbers. The genome of Mycobacterium massiliense strain M172 has been deposited in NCBI GenBank/DDBJ/EMBL under accession number AJSE00000000. The version described here is the rst version, which is available under accession number AJSE01000000.
ACKNOWLEDGMENTS
This work was supported by research grants UM.C/HIR/MOHE/08 and UM.C/625/1/HIR/004 from the University of Malaya, Kuala Lumpur, Malaysia.

REFERENCES
1. Adkambi T, et al. 2004. Amoebal coculture of Mycobacterium massiliense sp. nov. from the sputum of a patient with hemoptoic pneumonia. J. Clin. Microbiol. 42:54935501. 2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403 410. 3. Aziz RK, et al. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. 4. Grifth DE, et al. 2007. An ofcial ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am. J. Respir. Crit. Care Med. 175:367 416. 5. Kim H-Y, et al. 2010. Mycobacterium massiliense is differentiated from Mycobacterium abscessus and Mycobacterium bolletii by erythromycin ribosome methyltransferase gene (erm) and clarithromycin susceptibility patterns. Microbiol. Immunol. 54:347353. 6. McNerney R. 1999. TB: the return of the phage. A review of fty years of mycobacteriophage research. Int. J. Tuberculosis Dis. 3:179 184. 7. Zelazny AM, et al. 2009. Cohort study of molecular identication and typing of Mycobacterium abscessus, Mycobacterium massiliense, and Mycobacterium bolletii. J. Clin. Microbiol. 47:19851995.

Received 19 June 2012 Accepted 29 June 2012 Address correspondence to Siew Woh Choo, lchoo@um.edu.my, or Yun Fong Ngeow, yunngeow@um.edu.my. Copyright 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.01096-12

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